filler question

I am building a music stand out of cherry and curly maple -- the plans for the easel part call for a lap joint construction for the rails and stiles. Long story short, I have a hairline gap on the joint on one side. What's the best way to get rid of it? I was thinking rout a groove and put an inlay of something, maybe brazilian cherry to cover the joint. Obviously, I'd like to just fill it with something, but am pretty sure any sort of wood putty would be visible. I remember the guy who did my hardwood floors had some sort of stick (shellac?) that he would melt into a seam when it wasn't "quite right" and I was thinking that might work. This is pretty light wood though, and I was going to go with some sort of light analine dye. I've never used dye before, and don't know what would be the best filler material for that kind of coverage.